Where is your source? /usr/src/linux? If so then just try:
Code:
# make KSRC=/usr/src/linux/
However, I don't think this will work unless the source is for the kernel you are currently running, which is why ndiswrapper is looking for "/lib/modules/2.6.12-9-amd64-generic/build", usually a symlink to the current sources.
Doesn't Ubuntu have a package for ndiswrapper?